A proposed technique as a method of analyzing a transcriptome calculates a principal component from a data matrix of a change in expression level of the transcriptome, scales the principal component by dividing the principal component by a square root of the number of samples in the data matrix used for the calculation of the principal component or by a square root of the number of measurement items in the data matrix used for the calculation of the principal component, and specifies and selects a change in expression level at a predetermined threshold value from the scaled principal component (as described in, for example, JP 2012-039994A). This method is adaptable to data having different measurement items and having a large number of measurement items, such as transcriptome.
Another proposed technique uses a thermodynamic model to approximate a transcriptome formation mechanism and perform information processing of the transcriptome (as described in, for example, JP 2006-236011A). The thermodynamic model defines the concentration of each mRNA by using an energy parameter of determining a synthesis rate of each mRNA and an energy parameter of determining a degradation rate of each mRNA, and defines the energy parameter by using an intracellular local concentration of a factor having a base sequence-specific binding to RNA or DNA and a characteristic coefficient of a base sequence that is a possible target of the factor. At least one or more of the concentration of mRNA, the intracellular local concentration of the factor, and the characteristic coefficient of the base sequence are entered into the thermodynamic model, and the remaining values are calculated and outputted as unknowns. This linearly analyzes or estimates formation of the transcriptome.